wuepgg3-track 1.0.2

package/dist/models/TrackModel.d.ts

@@ -0,0 +1,142 @@
+import { TrackOptions } from "../types";
+interface ITrackModelMetadata {
+    "Track Type"?: string;
+    genome?: string;
+    [k: string]: any;
+}
+interface QueryEndpoint {
+    name?: string;
+    endpoint?: string;
+}
+/**
+ * Serialized track model, or the plain object argument to TrackModel's constructor.
+ *
+ * @example
+ * {
+ *     type: 'bigWig',
+ *     name: 'My bigwig track',
+ *     options: {
+ *         color: 'blue'
+ *     },
+ *     url: 'https://example.com',
+ *     metadata: {
+ *         genome: 'hg19'
+ *     }
+ * }
+ */
+interface ITrackModel {
+    name: string;
+    type?: string;
+    filetype?: string;
+    options: TrackOptions;
+    url?: string;
+    indexUrl?: string;
+    metadata?: ITrackModelMetadata;
+    fileObj?: Blob;
+    queryEndpoint?: QueryEndpoint;
+    querygenome?: string;
+    id: string | number;
+    label?: string;
+    files?: any;
+    details?: any;
+    isSelected?: any;
+}
+/**
+ * An object storing track metadata and state.
+ *
+ * @implements {Serializable}
+ * @author Silas Hsu
+ */
+export declare class TrackModel {
+    /**
+     * Makes a new TrackModel based off the input plain object.  Bascially does a shallow copy of the object and sets
+     * sets reasonable defaults for certain properties.
+     *
+     * @param {ITrackModel} plainObject - data that will form the basis of the new instance
+     */
+    name: string;
+    type: string;
+    label: string;
+    filetype?: string;
+    options: TrackOptions;
+    url: string;
+    indexUrl?: string;
+    metadata: ITrackModelMetadata;
+    id: number | string;
+    isSelected: boolean;
+    showOnHubLoad?: boolean;
+    fileObj?: any;
+    files?: any;
+    tracks?: TrackModel[];
+    querygenome?: string;
+    isText?: boolean;
+    textConfig?: any;
+    apiConfig?: any;
+    queryEndpoint?: QueryEndpoint;
+    legendWidth?: any;
+    details?: any;
+    constructor(plainObject: ITrackModel);
+    serialize(): this;
+    static deserialize(plainObject: any): TrackModel;
+    /**
+     * Gets this object's id.  Ids are used to keep track of track identity even through different instances of
+     * TrackModel; two models with the same id are considered the same track, perhaps with different options configured.
+     *
+     * @return {number} this object's id
+     */
+    getId(): number | string;
+    /**
+     * Gets the label to display for this track; this method returns a reasonable default even in the absence of data.
+     *
+     * @return {string} the display label of the track
+     */
+    getDisplayLabel(): string;
+    /**
+     * TODO: Document this.
+     *
+     * @param {string} term
+     * @returns {string}
+     * @memberof TrackModel
+     * always return a string
+     */
+    getMetadata(term: string): string | undefined;
+    /**
+     *
+     * @param term
+     * always return an array
+     */
+    getMetadataAsArray(term: string): string[] | undefined;
+    /**
+     *
+     * @param term
+     * @return return the meta value defined by user, maybe a string, an array or an object
+     * purpose of this is to allow users to customize metadata display, like defining colors
+     * in this way, for example
+     * Assay: {name: "ATAC-seq", color: "red"}
+     */
+    getMetadataAsis(term: string): any | undefined;
+    /**
+     * **Shallowly** clones this.
+     *
+     * @return {TrackModel} a shallow copy of this
+     */
+    clone(): TrackModel;
+    /**
+     * Shallowly clones `this` and `this.options`, and then modifies the clone's options.  Returns the clone.  This
+     * method will not mutate this instance.
+     *
+     * @param {string} name - the name of the option to set
+     * @param {any} optionValue - the value of the option
+     * @return {TrackModel} shallow clone of this, with the option set
+     */
+    cloneAndSetOption(name: string, optionValue: any): TrackModel;
+    /**
+     * Shallowly clones this and also selects a particular property to be cloned one level deeper.
+     *
+     * @param {string} prop - property name to also clone
+     * @return {TrackModel} shallow clone of this
+     */
+    _cloneThisAndProp(prop: string): TrackModel;
+}
+export default TrackModel;
+export declare function mapUrl(url: string): string | undefined;

package/dist/models/binning.d.ts

@@ -0,0 +1,29 @@
+/**
+ * implementing UCSC like binning schema in JS
+ * check http://genomewiki.ucsc.edu/index.php/Bin_indexing_system
+ * modified from tabix C code
+ * @author: Daofeng Li
+ */
+/**
+ *convert region to bin
+ *
+ * @export
+ * @param {*} beg
+ * @param {*} end
+ * @returns
+ */
+export declare function reg2bin(beg: any, end: any): number;
+/**
+ *convert region to bins
+ *
+ * @export
+ * @param {*} beg
+ * @param {*} end
+ * @returns
+ */
+export declare function reg2bins(beg: any, end: any): any[];
+/**
+ * atoms with hover event added
+ * add click event instead, hover seems slow
+ * @param {*} atoms2
+ */

package/dist/models/genomes/Creinhardtii506/Creinhardtii506.d.ts

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+export default Creinhardtii506;
+declare namespace Creinhardtii506 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from "./cytoBandIdeo.json";
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/CytobandTypes.d.ts

@@ -0,0 +1,17 @@
+/**
+ * A dictionary/mapping type that maps from chromosome name to a list of all cytobands in that chromosome.
+ */
+interface CytobandMap {
+    [chrName: string]: Cytoband[];
+}
+/**
+ * A single cytoband record.
+ */
+interface Cytoband {
+    chrom: string;
+    chromStart: number;
+    chromEnd: number;
+    name: string;
+    gieStain: string;
+}
+export default CytobandMap;

package/dist/models/genomes/GRCg7b/GRCg7b.d.ts

@@ -0,0 +1,17 @@
+export default GRCg7b;
+declare namespace GRCg7b {
+    export { genome };
+    export { navContext };
+    export const cytobands: {};
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/GRCg7w/GRCg7w.d.ts

@@ -0,0 +1,17 @@
+export default GRCg7w;
+declare namespace GRCg7w {
+    export { genome };
+    export { navContext };
+    export const cytobands: {};
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/GenomeConfig.d.ts

@@ -0,0 +1,16 @@
+import Genome from "../Genome";
+import NavigationContext from "../NavigationContext";
+import CytobandMap from "./CytobandTypes";
+import OpenInterval from "../OpenInterval";
+import TrackModel from "../TrackModel";
+export interface GenomeConfig {
+    genome: Genome;
+    navContext: NavigationContext;
+    cytobands: CytobandMap;
+    defaultRegion: OpenInterval;
+    defaultTracks: TrackModel[];
+    publicHubData: any;
+    publicHubList: any[];
+    annotationTracks: any;
+    twoBitURL?: string;
+}

package/dist/models/genomes/allGenomes.d.ts

@@ -0,0 +1,201 @@
+import { GenomeConfig } from "./GenomeConfig";
+/**
+ * All available genomes.
+ */
+export declare const allGenomes: ({
+    genome: import("..").Genome;
+    navContext: import("../NavigationContext").default;
+    cytobands: {};
+    defaultRegion: import("..").OpenInterval;
+    defaultTracks: import("..").TrackModel[];
+    twoBitURL: string;
+    annotationTracks: {
+        Ruler: {
+            type: string;
+            label: string;
+            name: string;
+        }[];
+        Genes: {
+            name: string;
+            label: string;
+            filetype: string;
+        }[];
+    };
+} | {
+    genome: import("..").Genome;
+    navContext: import("../NavigationContext").default;
+    cytobands: {};
+    defaultRegion: import("..").OpenInterval;
+    defaultTracks: import("..").TrackModel[];
+    twoBitURL: string;
+    annotationTracks: {
+        Ruler: {
+            type: string;
+            label: string;
+            name: string;
+        }[];
+        Genes: {
+            type: string;
+            name: string;
+            url: string;
+        }[];
+        RepeatMasker: {
+            "All Repeats": {
+                name: string;
+                label: string;
+                filetype: string;
+                url: string;
+                height: number;
+            }[];
+        };
+    };
+} | {
+    genome: import("..").Genome;
+    navContext: import("../NavigationContext").default;
+    defaultRegion: import("..").OpenInterval;
+    defaultTracks: import("..").TrackModel[];
+    twoBitURL: string;
+    annotationTracks: {
+        Ruler: {
+            type: string;
+            label: string;
+            name: string;
+        }[];
+        Genes: {
+            name: string;
+            label: string;
+            filetype: string;
+            url: string;
+        }[];
+        RepeatMasker: {
+            "All Repeats": {
+                name: string;
+                label: string;
+                filetype: string;
+                url: string;
+                height: number;
+            }[];
+        };
+    };
+} | {
+    genome: import("..").Genome;
+    navContext: import("../NavigationContext").default;
+    cytobands: {
+        chr1: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr2: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr3: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr4: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr5: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr6: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr7: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chr8: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chrM: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chrUn: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+        chrX: {
+            chrom: string;
+            chromStart: number;
+            chromEnd: number;
+            name: string;
+            gieStain: string;
+        }[];
+    };
+    defaultRegion: import("..").OpenInterval;
+    defaultTracks: import("..").TrackModel[];
+    twoBitURL: string;
+    annotationTracks: {
+        Ruler: {
+            type: string;
+            label: string;
+            name: string;
+        }[];
+        RepeatMasker: {
+            "All Repeats": {
+                name: string;
+                label: string;
+                filetype: string;
+                url: string;
+                height: number;
+            }[];
+        };
+    };
+})[];
+export declare const genomeNameToConfig: {};
+interface SpeciesConfig {
+    logoUrl: string;
+    assemblies: string[];
+    color: string;
+}
+export declare const treeOfLife: {
+    [speciesName: string]: SpeciesConfig;
+};
+/**
+ * @param {string} genomeName - name of a genome
+ * @return {GenomeConfig} the genome's configuration object, or null if no such genome exists.
+ */
+export declare function getGenomeConfig(genomeName: string): GenomeConfig | null;
+export declare function getSpeciesInfo(genomeName: string): {
+    name: string;
+    logo: string;
+    color: string;
+};
+export {};

package/dist/models/genomes/aplCal3/aplCal3.d.ts

@@ -0,0 +1,18 @@
+export default aplCal3;
+declare namespace aplCal3 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from "./cytoBand.json";
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/araTha1/araTha1.d.ts

@@ -0,0 +1,18 @@
+export default AraTha1;
+declare namespace AraTha1 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from './cytoBandIdeo.json';
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from '../../Genome';
+import TrackModel from '../../TrackModel';

package/dist/models/genomes/bosTau8/bosTau8.d.ts

@@ -0,0 +1,18 @@
+export default BosTau8;
+declare namespace BosTau8 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from './cytoBandIdeo.json';
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from '../../Genome';
+import TrackModel from '../../TrackModel';

package/dist/models/genomes/brapa/brara_chiifu_v3.0.d.ts

@@ -0,0 +1,17 @@
+export default BCHIIFUV3;
+declare namespace BCHIIFUV3 {
+    export { genome };
+    export { navContext };
+    export const cytobands: {};
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/calJac3/calJac3.d.ts

@@ -0,0 +1,17 @@
+export default CALJAC3;
+declare namespace CALJAC3 {
+    export { genome };
+    export { navContext };
+    export const cytobands: {};
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from '../../Genome';
+import TrackModel from '../../TrackModel';

package/dist/models/genomes/calJac4/calJac4.d.ts

@@ -0,0 +1,18 @@
+export default calJac4;
+declare namespace calJac4 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from "./cytoBandIdeo.json";
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/canFam2/canFam2.d.ts

@@ -0,0 +1,16 @@
+export default canFam2;
+declare namespace canFam2 {
+    export { genome };
+    export { navContext };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/canFam3/canFam3.d.ts

@@ -0,0 +1,18 @@
+export default canFam3;
+declare namespace canFam3 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from "./cytoBandIdeo.json";
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/canFam6/canFam6.d.ts

@@ -0,0 +1,18 @@
+export default canFam6;
+declare namespace canFam6 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from "./cytoBandIdeo.json";
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from "../../Genome";
+import TrackModel from "../../TrackModel";

package/dist/models/genomes/ce11/ce11.d.ts

@@ -0,0 +1,18 @@
+export default CE11;
+declare namespace CE11 {
+    export { genome };
+    export { navContext };
+    export { cytobands };
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+import cytobands from './cytoBandIdeo.json';
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import Genome from '../../Genome';
+import TrackModel from '../../TrackModel';

package/dist/models/genomes/danRer10/danRer10.d.ts

@@ -0,0 +1,17 @@
+export default DAN_RER10;
+declare namespace DAN_RER10 {
+    export { genome };
+    export { navContext };
+    export const cytobands: {};
+    export { defaultRegion };
+    export { defaultTracks };
+    export const twoBitURL: string;
+    export { annotationTracks };
+}
+declare const genome: Genome;
+declare const navContext: import("../../NavigationContext").default;
+declare const defaultRegion: import("../..").OpenInterval;
+declare const defaultTracks: TrackModel[];
+import annotationTracks from "./annotationTracks.json";
+import { Genome } from '../../Genome';
+import TrackModel from '../../TrackModel';

package/dist/models/genomes/danRer10/scaffolds.d.ts

@@ -0,0 +1,3 @@
+export default SCAFFOLDS;
+declare const SCAFFOLDS: Chromosome[];
+import Chromosome from '../../Chromosome';